Expect the Unexpected
by Queen of darkness.xo
Summary: A new threat rises that puts all life in the Galaxy at risk. After almost a year since Rachel's death, Chief continues the search for her. Reunited on the battlefield Chief is confused as to why she is fighting for the other side. Enemies become allies.
1. Prologue

**Author's notes : Hello everyone ! So, this is the second installment to the fan fiction about Master Chief and Lieutenant Rachel Fleming. If you haven't read the first story, then you may not understand some things in this one. For those of you who read and enjoyed the first one, here's the second one as promised ! I hope you enjoy it ! **

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><p>A soft hum traveled through a well lit, well ventilated room. The walls were cast in a marble-like material. Holographic monitor's and terminals adorned one of the walls. Seats were cast off in different directions around the room, and there were different instruments that hung suspended in the air attached to a cord-like apparatus, ready to use.<p>

The most important part of the room however, would be the bed-like structure extending from one of the walls, hovering in the air with what appeared to be an incubator attached to it. The force-field like incubator that hummed to life around the being inside was of different hues of purple's and blues with the occasional red.

Laying in the suspended medical incubator was a female human. Her long brown hair cascaded down the sides of her face, her eyes closed. Dressed in what would be the equivalent to human bandages and clothes, she was covered up. Her chest slowly rose and fell as she took in each breath, but she appeared to be in a state of coma.

"How are her vitals?" a male voice asked.

"Her vitals are good. Her breathing and blood pressure are both stable, and her flesh wounds were easily healed. " another answered.

" Good. What's the status on brain damage?" the first male asked again, looking at the woman suspended in the bed.

The other was silent for a moment as he pressed a few different hieroglyphic buttons on the terminal in front of him displaying what would be the equivalent to human charts and readings.

"Beyond flesh wounds and standard repairs, we don't quite have the proper understanding on how to deal with a human. We don't know their anatomy all too well, or how it specifically works." the male, presumably the doctor asked.

The other man was silent. The mandibles on his face moving slightly as his eyes were focused on the woman. He, as well as the doctor were both Elite's, or Sangheli's. A covenant race. The man in charge was Rha 'Mantakrea. He was the leader of the general populace, dealing more with the army battalion's. He would be what a General would be in human terms, but he also held status of a political leader as well. The doctor, well his name wasn't important.

" Sir, our best option would be to contact the humans and let them know about this woman. They would be able to take her and heal her properly. " the doctor suggested.

Rha sighed. " We cannot contact the humans, you know what is at risk. " he said.

" Then I don't know how much help we can be to her." the doctor said.

Rha stood there, his eyes scanning over the reports again and back to the woman who lay there. He watched as her chest rose and fell slowly. Walking over to the encased woman, his eyes never left her. Humans were an intriguing species. Rha could see how soft the woman's skin was and he wondered how a species so soft and almost seemingly fragile could be so fearsome and strong. Though, she was different, special. She survived what most humans couldn't. Mostly thanks to her suit, but her body was strong, reinforced.

" She's alive, and for now that's good enough ." Rha said turning away from her and heading towards the exit.


	2. Innocent Until Proven Guilty

**Master Chief**

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><p>"This is bullshit !" A man clad in a white uniform, decorated with an assortment of medals and accommodations shouted.<p>

" Calm down admiral. " Another voice spoke of a man who wore similar attire with even more medals, proving he was higher in authority.

" You're just going to let this SPARTAN off with no charges, no responsibility, no nothing?" The first man spoke.

" This SPARTAN saved Earth and the entire of the human race, the galaxy, more times than any of us can count! And you want to condemn him ? To shut him off and put him away ! To punish him for everything that he has done ? another spoke up, his uniform also decorated with accommodations.

" He killed marines ! He killed a commanding officer ! He's a monster. There's no telling what he could do if he decided to turn against all of us ! We couldn't stop him !"" the first spoke up .

" That commanding officer allowed experiments against our own people to go on ! He helped in the destruction of precious lives and the development of another threat that could have destroyed the entire universe ! He would never turn against his own people." the third man spoke, still defending Master Chief.

" Enough ! Both of you !" the leading chairman finally spoke, quieting the others. " Yes, Master Chief otherwise known as SPARTAN - 117, has committed an offence against the UNSC in an act of treason of murdering a commanding officer when he should have brought him in to face a fair and proper trial. " he began. " However, Master Chief has proven on more than one occasion that he is fiercely allied with the UNSC, Earth and all her inhabitants. He fights for all the right reasons, and has saved our asses more times than we can thank him for. Therefore, he is being let off on no charges and instead granted the Medal of Honor. He is to resume duty with his unit and carry on fighting for the UNSC and against all threats to the Human race. " he said as he stood. " Dismissed. " he spoke in finality, exiting the room.

The man who had defended Chief stood with a big grin on his face as he exited the room happy, glad that justice had been served and that Chief wouldn't be reprimanded. The other man however, was not pleased.

-

"Chief. " Cortana's voice rang out through the room.

Chief stood on the opposite side, looking out the window at the stars and various UNSC ships that surrounded them. He didn't answer her at first, half wanting to know the answer she had for him but at the same time not wanting to know. Ever since they left that planet, and left Rachel behind, he had been getting Cortana to search for any kind of information that would help them get back to that system so they could go to the planet, and he could find Rachel.

A few weeks back, Cortana had finally figured out what system it had been in. Of course, Chief had been under strict lock down and observation while his case was settled within the UNSC courts. He didn't care about that though, he regretted nothing and would kill the commander ten times over if he had the chance. While all the uniforms sat in a room and decided his fate, there was only one thing that he cared about.

Finding Rachel.

Cortana had sifted through the known planets that had been documented by the UNSC, and Chief was just awaiting the status of the planet. The moment he figured out where he was he would find the nearest ship and plot the course to it. However, something within him said that he wasn't going to like the news that she had.

"Chief." her voice came again, this time he turned his head to the side, seeing the holographic image of Cortana on the console across the room. " I've located the planet. ." she started.

Chief could tell right away by her tone, and how she trailed off that whatever followed wasn't going to be good. So he braced himself.

" Recent reports and images show that.. it's been glassed." Cortana finally said.

Chief felt his heart sink at this news. Finally he had located the planet, after so many months of searching only to find out that it had been glassed. Was the alliance they made with the Sangheli terminated without his knowledge? Had they betrayed the humans ? Or were they simply unaware of it in systems far away ? Whatever the reason he felt as though he needed to take out his anger on someone, something. Anything. Human, Brute, Elite, Grunt, Jackal, Hunter.. it didn't matter. Something needed to die at his hands. Hell, he would charge into a horde of flood right then and there if it were possible.

" I'm sorry Chief... youv'e done everything you could have." she said sympathetically.

" No, I didn't." Cheif answered in his monotone voice.

" Good news !" A man shouted as the doors to the room opened, and the colonel entered with a smile pressed on his face. " I just came back from the final meeting, and you're off the hook Chief. You are to return to duty A.S.A.P. " he said as he approached the Spartan.

Chief glanced over at him. " Whens my next mission?" he asked.

" Well... right now if you're willing." the colonel answered.

" What is it?" he asked.

"Well, there's been a lot more attacks by Brutes in the unicorn system. The motive of their attack is unknown, for there is no valuable resources or technologies on the planet Cronkee. It was part of the war near first contact. Simple excavating teams, and some patrols remain there. All the camps have been hit and the people missing. There's no bodies, save for some marines that tried to fend off the attack but.. we're talking a quarter of a fleet of Brutes attacking these small camps. The marines stood no chance. " the Colonel said. As he spoke, images of the planet and the empty camps were displayed on the screen in the room they were in. " We're sending in a strike team to find these prisoner's and bring them back. However, against Brute's were going to need some of the best. That's why you're heading this mission with the black ops core as your back up. We have ships on the way now to defend any kind of incoming battle ships. You leave at 14:00." The colonel said as he turned and exited the room, leaving Cortana and Chief.

Without wasting time, Chief approached the wall opposite the screen and the terminal that Cortana was in. On it was several rows of weapons. Picking up an assault rifle, a pistol and several grenades he equipped them to himself, and checked to make sure that his weapons were full of ammo.

Looking over at the image of Cortana he paused. " You coming ?" he asked her.

" As if I can trust you on your own." she answered.

He went over to the terminal and removed the chip that she was in .Placing it in the back of his helmet, he cocked his gun and exited the room. Ready to take out his anger and any being that opposed him.

-

Leading the black ops team through the camp left behind by the marines that were there before them, Cheif was alert in case there were any Brutes around watching them. The others followed closely behind him, he knew that they too were alert and cautious of their surroundings, prepared for any surprise attacks.

Looking through the camp, there was nobody there. There was the odd marine corpse, but that was it. None of the documents or files were touched, and weapons were left behind. Chief didn't know what to make of it. It didn't make any sense to him. Why would they take human prisoners?  
>"Brutes are known for taking prisoners, but they don't last long." Cortana said as if thinking the same thing that Cheif was. " But, what would their purpose be? Ransom maybe. " she said. " Still..ransom for what? It's not like they want money, and the issue with the halo rings has been resolved - more or less. What could they possibly want?" she said.<p>

Cheif thought the same, but bore no answers for her.

"Sir !" one of the marines said. " We've got tracks, and they led into the jungle." he said.

" Tracks means they weren't picked up by a drop ship. This is odd behavior for Brutes. " Cortana said.

" Yeah. What I want to know is, who's leading them?" Chief asked. The prophet was dead, the halo rings unusable for the most part. What could the brutes possibly want? And were any of them smart enough to lead the entire of the race?

" Follow the tracks and stay sharp. Watch you six and report anything you see. Keep your eyes open marines." Chief said as he began to follow the tracks, the marines following behind him. Their weapons trained on the tree's, hills and any inconspicuous areas.

For quite a few hundred meters there was no activity, but the footprints continued on. Chief was still cautious as he led the team. When the footsteps suddenly stopped, he raised his hand to stop the others as they complied and had their weapons trained in several different directions in their small area.

Taking a few more steps forward, Chief scanned the area and checked the radar on his HUD. There was nothing.. but that didn't mean that something wasn't there. Chief knew better than to just rely on the instruments they were given to track enemies. He had instincts, and right now his instincts were saying they weren't safe.

Turning his head slightly he could have sworn he heard heavy breathing but the clearing was still clear. Then there was a footstep and his weapon was instantly trained on the area in which it came, but still nothing was there.

Then he saw it, the shift in the air. The distortion of the air in a certain area gave away the position of the one lurking. Aiming for where the head on this creature would be, Chief pulled the trigger and the sound of his assault rifle filled the silence in the air. A loud groan was heard as a Brute materialized and fell to the ground, dead.

" Check your surroundings, they're camouflaged!" Chief said notifying the others as they all had their weapons trained searching for any shift in the air.

" Found one!" one of the operatives said as he pulled the trigger and took down another camouflaged Brute.

The Brutes decided to act as they charged out from the tree's and knocked away what weapons they could, pinning the humans to the ground. Chief took out the ones that came into his vision, and turned on his heel delivering a knee to the chest of one of the brutes holding down an operative knocking him back and the proceeding to fill his chest with bullets. The Brute's continued to attack, growing in number.

Grabbing and incapacitating the humans, Chief did his best to take down who he could but they were out numbered ten to one.

" Retreat!" Chief shouted as him and the agents began to move backwards slowly, shooting the brute's so they wouldn't get any closer. Chief did his best to get to the agents that were pinned to the ground by the Brute's but there was no way he could get to them without risking getting caught himself.

Cursing under his breath he had no choice but to leave them as he led the team away from the ambush and through the tree's, finally out in the open where the marine camp was. They had a Pelican waiting to pick them up. Running, Chief stopped as he reached the Pelican and turned providing cover fire so the rest of the team could get into the Pelican. Once everyone was in, he jumped in and watched as the Brute's came barreling through the jungle into the camp. Seeing them escape, they let out a long howl as they were clearly dissatisfied with their escape.

Chief watched as they left orbit, aggravated at what had just occurred... and confused.

**Author's notes : Chapter two is done. It seems a bit slow I apologize but it serves it's purpose for setting things up I promise it will get much better :) WELLLL. You know what to do. REVIEW. :D 3**


	3. Upgrade

**Author's notes: I know. I know . You all probably hate me for taking forever. But I did not forget about this story, still have lots of it written up and the plot finished I have just been busy with working.**

**Rachel**

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><p>Rays of sun shone through the large window of the room that was located on the second floor of the generals personal home. Laying on the bed centered against the opposite wall from the window, was Rachel the only human on the home world of the Sangheli, better known as the ' Elites '.<p>

Rachel stirred as her golden brown eyes slowly opened. For a few moments she remained still, her body was sore and her mind was still trying to process waking up. Letting out a small moan of pain she slowly lifted her arms and looked at her hands in front of her face, taking in the uninjured appearance of them. Placing her arms beneath her she slowly lifted herself up letting out a few more groans of pain. Resting her back against the bed she looked around the room she was in. Confused, she had no idea where she was. The furniture and decorations were unfamiliar to her as well as the view from the window.

Pushing the blankets aside she tried to swing her legs over the side of the bed so she could get up and figure out where she was. Moving slow she started with one leg, and then the other. Sliding herself off the bed she grabbed what would be the equivalent to a nightstand and hoisted herself up. Her legs instantly gave out as she fell to the ground, letting out a small yelp of pain.

It was then that the door opened and a Sangheli entered carrying a tray of what appeared to be food. Seeing Rachel fall, the Sangheli let out a worried noise and placed the tray on a table to rush over to Rachel's side. At the sight of the Elite, Rachel's eyes widened as she tried to move to get away but she didn't have much strength to do so.

" Please, do not move. You're not fully healed yet." The female Elite spoke in a calm tone. " I'm here to help you." she added.

Rachel didn't say anything at first. Still weary of the females help, she slowly reached out her hand . There really wasn't anything else she could do at the moment. Even if the Elite was there to harm her it wasn't as though Rachel could get away, but if the Elite was offering help than the least she could do was try to see if it was genuine.

The female took Rachel's hand and slowly lifted her, helping her back onto the bed. Pulling the blankets over Rachel she walked over to the tray she carried in previously and brought it back to Rachel. " My name is Serah'Resaree." she began. " I am the wife of General Rha'Mantakrea. The one who saved you." she explained.

"Saved me?" Rachel finally spoke, her voice hoarse.

"Yes." Serah answered. " Back on that planet, Rha went to deliver the message to the others that we are no longer at war. When he got there, he saw the explosion of your human facility. He said he found you shielded by some sort of energy force. There were no other humans around and because of the flood threat, the planet had to be glassed. Rha said he wasn't going to leave you there." she finished.

Rachel was silent, taking in all that she had said. Looking down at her legs, she stared at her knee's for no apparent reason other than the fact it was where her gaze fell. It remained there for a while as she was still trying to get a grasp on the situation. Rachel never expected to survive let alone be saved and nursed back to health by the Sangheli. Even though they were allies, it still felt wrong.

"Are you okay?" Serah spoke up.

Rachel looked up at her, her gaze still solemn and her mind full of thoughts. Rachel didn't quite know how to answer her, was she okay? She herself didn't know.

" I understand it is a lot of information. I will leave you to rest now human." she spoke as she turned to exit.

" Rachel. " her voice called through the room. Serah turned and looked at her. " My name, is Rachel."

Serah nodded her head. " Rest well Rachel. I will be back later to check up on you." she said and then exited the room, the door shutting behind her.

Rachel sighed as she leaned back, her head resting against the bed. Staring up at the cieling she continued to think about everything that had happened. The last memory she had was seeing Chief fly off into space and then the facility exploded and nothing after that. Although she activated her shield lock, she never thought it would work to the extent that it did it was merely just a last minute action in which she thought was in vain.

Apparently, it worked better than she expected.

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><p><strong>Master Chief<strong>

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><p>" This is.. disturbing news. " The admiral said over the comm as Chief had reported the mission details to him. " Never before have we heard of the Brute's acting so strategically. With the Prophets dead and the war at an end we thought they would just disperse and fight for leadership and colonies. However, we never expected them to strike out at the human's again. It leads me to wonder who is leading them, and why. With the halo rings under our control and the device to activate them destroyed... it just doesn't make sense. " The admiral concluded.<p>

" I've already searched through the data base of the known Brute's that have high status, but it says they all died in the war. " Cortana spoke up, her holographic form shining through the nearby terminal. " They are still at odds with the Sangheli's . There have been a few fights between the two races in some of the far off systems, but nothing that has interfered with the UNSC. Only the recent attack on the research camps." she spoke.

" Is it possible they're after our research and intelligence?" The admiral asked.

" It's possible but.. unlikely. The Brute's aren't exactly the most intelligent race. They're very feral and instinctive, fighting for power and survival. There have been no Brute scientist or doctor's to date. The intelligence fell under the Sangheli leadership and the rule of the Prophets. This is why the Brute's were always used as front line attackers. " Cortana explained.

" If the Brute's don't want the information than they're working for someone who does. That someone has to be either Sangheli, human or another Prophet. " Chief explained. " I highly doubt it's a human or an Elite so that only means that there's another Prophet out there leading these Brute's. " he said.

The admiral nodded." And if what you said is true, about them taking live captives than we can assume they are experimenting on them. Perhaps we're looking at some sort of biological warfare here. Chief, I want you to stay on this mission. Find out who is leading these Brutes and kill them before they have a chance at striking out against us. " he ordered.

" Yes sir." Chief answered with a nod of his head.

" We will send you the co-ordinates of the place we think they will attack next. I'll be awaiting your report. Dismissed. " and with that, the admiral disappeared.

Chief walked over to the window of the ship and looked out at the stars. He was silent. Thinking about the situation he didn't have a good feeling about any of it. The previous missions he was given, the war that he was a part of, he had a clear cut objective. They knew what they were up against and they knew how to stop it. Now however, they were left in the dark and going on hunches and ' maybe's '. Chief hated that. Even though he would do as instructed, he would feel better knowing who the true enemy was.

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><p><strong>Rachel<strong>

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><p>"Well, what do you think ?" Rha asked as he looked at Rachel.<p>

Her eyes widened as she took in the image in front of her. Suspended in an anti-gravity field was her suit. Although, it was different than before. Other than the fact that it looked really cool, she could tell that they improved her suit and added a lot to it. It still held the basics of the SPARTAN armor, but with the alien technology it looked as though it was alive.

" That looks.. awesome. " She finally commented.

" Awesome?" Rha questioned as he looked to the Sangheli that was beside him who simply shook his head. " I am unfamiliar with this human term.. is it a positive reaction ?" he questioned her.

Rachel looked up at him with a small smirk as she nodded her head. " Yes. Awesome is a good thing. It's a word that means..." she paused. " Well..awesome." she said with a shrug. " I love it. " she said again.

" You are pleased? Then I am glad. " he said with a nod of his head. " We have not been able to duplicate the design of the suit, we were however able to upgrade it using both covenant and forerunner technology. Surprisingly, the forerunner technology bonded better with the suit than the covenant technology did." he spoke as diagrams appeared on the terminals before them breaking down the suit. " We added a the suit with a plasma core. This means your shields will last longer. We've also upgraded your radar so that it is similar to the ones we have on our ships. "he said as the screen changed. " Also, the right arm has an interchangeable plasma cannon in it . You can activate it through the command in your helmet . The core has been used to power most of the suits functions that was destroyed from the blast. The blue veins that you see throughout the suit are where the tubes were put in to circulate the plasma. " he explained as the suit glowed from the blue veins. " It was the best we could do as we do not have the same machines or blueprints that originally created this suit." he explained to her.

" This is.." she started as she circled the suspended armor. " Thank you Rha.. I am in your debt." she said to him as she looked at the General.

And she meant it.


End file.
